The assumption is that Hiyuki is going to join the main characters and oppose Soga but what if

She is a faction on to her own. She believed in the Kamunabi and even when she confronted Chihiro she never sided with him. Instead she allowed and vouched him to join the Kamunabi.

However, I can't see her siding with a Soga who is planning on using the enchanted blades. She was totally against that in first place.

Very similar to how Marco took on the Blackbeard pirates with the remnants of the whitebeard pirates after whitebeard died, She has her own TRUE Kamunabi that doesn't align with what Chihiro wants to do but could temporarily ally for common things against the Soga run Kamunabi.

It could be Chihiro and his new EB blade wielders, Hiyuki and the Taiwan Kamunabi that was forced to exile made up of her and possible other clans who don't want to be exteriminated and Soga/Hishaku/Kamunabi blend all creating some sort of stalemate sort of like Yonkou/WG/Shichibukai again from One Piece